Jasper Butcher
24f2fb17bc
Merge pull request #38 from RosettaCommons/rac_docs
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Add example input files and update documentation for RFD3
2025-12-03 20:38:58 -08:00
Jasper Butcher
5233cadb89
Merge branch 'production' into rac_docs
2025-12-03 20:38:08 -08:00
Aiko Muraishi
ffb0bcf2a7
fix: some bugs in legacy parsing and symmetry
2025-12-03 19:14:52 -08:00
Aiko Muraishi
d9334d7075
symmetry.md updated
2025-12-03 17:38:43 -08:00
Jasper Butcher
7f6656ebf4
Merge pull request #37 from RosettaCommons/readme-fixes
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Update README
2025-12-03 17:13:05 -08:00
jbutch
3aa634158d
Minor updates to readme
2025-12-03 17:12:19 -08:00
jbutch
27126f0f17
Add new file
2025-12-03 16:39:58 -08:00
Jasper Butcher
536af6eff4
Update README.md
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com >
2025-12-03 15:39:54 -08:00
Rachel Clune
20e8105a79
Add example input files and update documentation for RFD3
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Added example JSON input files for enzyme, protein binder, and small molecule binder design in models/rfd3/docs. Updated corresponding markdown documentation to include instructions for running these examples and clarified usage details. Expanded README with more detailed setup, inference, and training instructions, including HBPLUS installation steps.
2025-12-03 15:19:17 -08:00
Rachel Clune
5582c7d248
Fix checkpoint directory flag in installation command
2025-12-03 14:50:04 -08:00
jbutch
ab6b438137
Update README
2025-12-03 14:16:41 -08:00
Rohith Krishna
6d18903e43
Merge pull request #36 from RosettaCommons/feat/collab
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feat: collab notebook
2025-12-03 10:52:24 -08:00
Rachel Clune
70c6b2c4e2
Fix command option for checkpoint directory
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Updated the command syntax for installing models.
2025-12-03 10:00:38 -08:00
ncorley
04cb7f2ca6
feat: collab notebook
2025-12-03 09:31:41 -08:00
Rohith Krishna
395737750a
Merge pull request #32 from RosettaCommons/fix/readmes
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Add assets, cleanup READMEs, remove old files
2025-12-03 02:45:31 -08:00
Nathaniel Corley
48d7d565c4
Merge pull request #34 from RosettaCommons/inference-runner
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fix: remove rootutils from inference.py
2025-12-03 02:42:36 -08:00
Rohith Krishna
51c6228072
Merge pull request #35 from RosettaCommons/fix/notebook
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fix: notebook
2025-12-03 02:39:49 -08:00
ncorley
97a803d1c4
fix: notebook
2025-12-03 02:37:54 -08:00
Rohith Krishna
bae631b9b4
force include yamls for inference
2025-12-03 02:35:36 -08:00
ncorley
3106504ae1
fix: notebook
2025-12-03 02:25:06 -08:00
Rohith Krishna
86137ef3ed
fix: remove rootutils from inference.py
2025-12-03 02:17:30 -08:00
Ubiquinone-dot
2da0087880
Add file
2025-12-03 01:52:12 -08:00
Ubiquinone-dot
7c8a29437b
Add assets, cleanup READMEs, remove old files
2025-12-03 01:50:50 -08:00
Rohith Krishna
eb4f8ab83e
Merge pull request #33 from RosettaCommons/fix/checkpoints
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chore: ruff, fix checkpoint code
2025-12-03 01:50:44 -08:00
ncorley
1bf46afa21
chore: ruff, fix checkpoint code
2025-12-03 01:48:46 -08:00
Rohith Krishna
d14203b264
Merge pull request #31 from RosettaCommons/fix/rootutils
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remove use of rootutils to allow for pypi
2025-12-03 01:17:01 -08:00
Rohith Krishna
7668d03d04
use .foundry as default for checkpoint dir
2025-12-03 01:15:23 -08:00
Rohith Krishna
c859ce4fc0
remove use of rootutils to allow for pypi
2025-12-03 01:12:14 -08:00
Rohith Krishna
5ae1567d3a
Merge pull request #30 from timkartar/patch-1
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Make trajectory png slightly bigger
2025-12-03 00:53:02 -08:00
Raktim Mitra
fc9aea95a2
Merge branch 'RosettaCommons:production' into patch-1
2025-12-03 00:51:40 -08:00
Raktim Mitra
30231f1457
Update README.md
2025-12-03 00:50:53 -08:00
Rohith Krishna
31cedb1d0a
Merge pull request #29 from timkartar/patch-1
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Update README.md fix trajectory.png link
2025-12-03 00:50:35 -08:00
Raktim Mitra
46eeaa45f0
Update README.md fix trajectory.png link
2025-12-03 00:47:49 -08:00
Rohith Krishna
e79dcb71ab
Merge pull request #28 from RosettaCommons/stage_for_production
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Stage for production
2025-12-03 00:35:28 -08:00
AndrewKubaney
dfe5402a5d
add in weights docs and help string fix ( #727 )
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* chore: add SolubleMPNN, additional warnings, wts.
* fix: fix --help string option.
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Co-authored-by: Andrew Kubaney <akubaney@localhost>
2025-12-03 00:34:46 -08:00
Rachel Clune
98b12108c7
Added details and fixed typos in NA binder design examples ( #721 )
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* Fixed spelling and grammar mistakes in the md file for NA binder design examples. Created a .json file containing the code bits for users to easily run the examples.
* NA example clean up
Removed NA examples from foundry docs directory and moved necessary files to the RFD3 docs directory. Added example syntax for how to use `rfd3 design` instead of `python ...`
* Update na_binder_design.md small edits to the hbplus warning sentence
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Co-authored-by: Raktim Mitra <timkartar7879@gmail.com >
2025-12-03 00:34:46 -08:00
Nathaniel Corley
d72e49aa96
docs: dataset readme ( #726 )
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* docs: dataset readme
* more docs for training
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Co-authored-by: Rohith Krishna <rohith@localhost>
2025-12-03 00:34:46 -08:00
Jasper Butcher
94bb987998
Refactor/checkpoint defaults ( #723 )
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* Registry rework
* Update README 12
* Mc
* Add all option correction
2025-12-03 00:34:45 -08:00
Rohith Krishna
d07d003ae2
remove notebook outputs
2025-12-03 00:34:45 -08:00
Rohith Krishna
2cd401665b
initial progress on documentation cleanup ( #722 )
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* initial progress on documentation cleanup
* formatting input.md
* docs: more documentation for ppi and sm binder design
* fix typo
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Co-authored-by: Rohith Krishna <rohith@localhost>
2025-12-03 00:34:45 -08:00
Nathaniel Corley
5ec34da7c1
chore: fix regression tests for rf3 ( #725 )
2025-12-03 00:34:45 -08:00
Rohith Krishna
adb11204c8
remove more instances of foundry ( #724 )
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Co-authored-by: Rohith Krishna <rohith@localhost>
2025-12-03 00:34:45 -08:00
Raktim Mitra
3414c0e833
Refactor/sm binder cleanup ( #720 )
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* remove dialect key, and exposed case
* change hbplus metric fail log to warning from error
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Co-authored-by: Raktim Mitra <raktim@digs.ipd.uw.edu >
2025-12-03 00:34:45 -08:00
Raktim Mitra
264bb79ee4
hbplus_instruction ( #719 )
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Co-authored-by: Raktim Mitra <raktim@digs.ipd.uw.edu >
2025-12-03 00:34:45 -08:00
Rohith Krishna
faa2935417
remove ipd specific files
2025-12-02 20:56:06 -08:00
Rohith Krishna
bf8b44a83f
feat: enable installing checkpoints from command line
2025-12-02 20:29:09 -08:00
Rohith Krishna
db7cbf37d1
fix: fix path in paths for pdb parsing ( #715 )
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* refactor: change modelhub to foundry
* fix: fix path in paths for pdb parsing
* Update run_inf_tutorial.sh
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Co-authored-by: Rohith Krishna <rohith@localhost>
Co-authored-by: Raktim Mitra <timkartar7879@gmail.com >
2025-12-02 17:55:02 -08:00
Jasper Butcher
62cbbe28e5
Finalizing READMEs ( #711 )
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* Draft update to main
* Minor changes
* Add files
* ppi/sm/enzyme.md and input.md/reade.md cleanups
* fix run commands
* fix: typo in ppi md
* fix: Update header dna_binder_design.md
* description of dna_binder_design examples in .md
* fix: Update dna_binder_design.md fix typo
* fix: Update main README.md to add all citations
* fix: filename dna->na
* fix: filename dna->na
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Co-authored-by: Raktim Mitra <raktim@digs.ipd.uw.edu >
Co-authored-by: Raktim Mitra <timkartar7879@gmail.com >
2025-12-02 16:46:33 -08:00
Rachel Clune
76e61e0c2d
docs: update RFD3 README ( #714 )
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* Added more explanation and fixed small issues in demo commands in RFD3 README
* fix github actions grepping ruff
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Co-authored-by: Rohith Krishna <rohith@localhost>
2025-12-02 16:42:04 -08:00
Nathaniel Corley
050390fd67
Feat/notebook and rf3 confidence refactor ( #713 )
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* chore: ruff
* feat: rf3 confidence, notebook update
2025-12-02 16:26:38 -08:00
